{"metadata": {"kernelspec": {"name": "mindspore-python3.7-aarch64", "display_name": "MindSpore-python3.7-aarch64", "language": "python"}, "language_info": {"name": "python", "version": "3.7.6", "mimetype": "text/x-python", "codemirror_mode": {"name": "ipython", "version": 3}, "pygments_lexer": "ipython3", "nbconvert_exporter": "python", "file_extension": ".py"}}, "nbformat_minor": 5, "nbformat": 4, "cells": [{"cell_type": "code", "source": "#\u5bfc\u5165\u4ee3\u7801\u548c\u6570\u636e\nimport os\nimport moxing as mox\ndata_obs_url = 'obs://bdci2022/unet' \ndata_local_url = './'\nmox.file.copy_parallel(data_obs_url,data_local_url)\nprint('\u4ee3\u7801\u548c\u6570\u636e\u5bfc\u5165\u5b8c\u6210....')", "metadata": {"trusted": true}, "execution_count": 1, "outputs": [{"name": "stderr", "text": "INFO:root:Using MoXing-v2.0.0.rc2.4b57a67b-4b57a67b\nINFO:root:Using OBS-Python-SDK-3.20.9.1\nINFO:root:Listing OBS: 1000\nINFO:root:Listing OBS: 2000\nINFO:root:Listing OBS: 3000\nINFO:root:Listing OBS: 4000\nINFO:root:Listing OBS: 5000\nINFO:root:Listing OBS: 6000\nINFO:root:pid: None.\t1000/4939\nINFO:root:pid: None.\t2000/4939\nINFO:root:pid: None.\t3000/4939\nINFO:root:pid: None.\t4000/4939\n", "output_type": "stream"}, {"name": "stdout", "text": "\u4ee3\u7801\u548c\u6570\u636e\u5bfc\u5165\u5b8c\u6210....\n", "output_type": "stream"}]}, {"cell_type": "code", "source": "!ls", "metadata": {"trusted": true}, "execution_count": 2, "outputs": [{"name": "stdout", "text": "bdci.ipynb  pred.py\t\t   requirements.txt\t    Untitled.ipynb\nDockerfile  preprocess_dataset.py  src\neval.py     README_CN.md\t   train.py\nkits19\t    README.md\t\t   unet_simple_config.yaml\n", "output_type": "stream"}]}, {"cell_type": "code", "source": "!pip install SimpleITK==2.2.0 -i https://pypi.tuna.tsinghua.edu.cn/simple", "metadata": {"trusted": true}, "execution_count": 3, "outputs": [{"name": "stdout", "text": "Looking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple\nCollecting SimpleITK==2.2.0\n  Downloading https://pypi.tuna.tsinghua.edu.cn/packages/cc/50/23b9a47f1098a58712340690e253c82b4f9248ac4b18d129ab639db21506/SimpleITK-2.2.0-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (48.1 MB)\n\u001b[K     |\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 48.1 MB 29 kB/s  eta 0:00:01     |\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2589              | 26.8 MB 4.0 MB/s eta 0:00:06\n\u001b[?25hInstalling collected packages: SimpleITK\nSuccessfully installed SimpleITK-2.2.0\n", "output_type": "stream"}]}, {"cell_type": "code", "source": "!pip install -r requirements.txt", "metadata": {"trusted": true}, "execution_count": 4, "outputs": [{"name": "stdout", "text": "Looking in indexes: http://repo.myhuaweicloud.com/repository/pypi/simple\nRequirement already satisfied: opencv-python>=4.1.2.30 in /home/ma-user/miniconda3/envs/MindSpore-python3.7-aarch64/lib/python3.7/site-packages (from -r requirements.txt (line 1)) (4.2.0.34)\nRequirement already satisfied: pillow>=6.2.0 in /home/ma-user/miniconda3/envs/MindSpore-python3.7-aarch64/lib/python3.7/site-packages (from -r requirements.txt (line 2)) (7.0.0)\nRequirement already satisfied: numpy in /home/ma-user/miniconda3/envs/MindSpore-python3.7-aarch64/lib/python3.7/site-packages (from -r requirements.txt (line 3)) (1.17.5)\nRequirement already satisfied: pyyaml in /home/ma-user/miniconda3/envs/MindSpore-python3.7-aarch64/lib/python3.7/site-packages (from -r requirements.txt (line 4)) (5.3.1)\n", "output_type": "stream"}]}, {"cell_type": "code", "source": "!python preprocess_dataset.py --raw_data_path=kits19 --data_path=dataset # \u6570\u636e\u9884\u5904\u7406 3D -> 2D slices", "metadata": {"trusted": true}, "execution_count": 5, "outputs": [{"name": "stdout", "text": "{'enable_modelarts': 'Whether training on modelarts, default: False', 'data_url': 'Dataset url for obs', 'train_url': 'Training output url for obs', 'checkpoint_url': 'The location of checkpoint for obs', 'data_path': 'Dataset path for local', 'output_path': 'Training output path for local', 'load_path': 'The location of checkpoint for obs', 'device_target': 'Target device type, available: [Ascend, GPU, CPU]', 'enable_profiling': 'Whether enable profiling while training, default: False', 'num_classes': 'Class for dataset', 'batch_size': 'Batch size for training and evaluation', 'weight_decay': 'Weight decay.', 'keep_checkpoint_max': 'keep the last keep_checkpoint_max checkpoint', 'checkpoint_path': 'The location of the checkpoint file.', 'checkpoint_file_path': 'The location of the checkpoint file.', 'train_augment': 'Whether apply data augment when training.'}\n{'FixedLossScaleManager': 1024.0,\n 'batch_size': 16,\n 'checkpoint_file_path': 'ckpt_unet_simple_adam-4-75.ckpt',\n 'checkpoint_path': './checkpoint/',\n 'checkpoint_url': '',\n 'color': [[0, 0, 0],\n           [255, 0, 0],\n           [0, 255, 0],\n           [0, 0, 255],\n           [0, 255, 255],\n           [255, 0, 255],\n           [255, 255, 255]],\n 'config_path': '/home/ma-user/work/src/model_utils/../../unet_simple_config.yaml',\n 'crop': 'None',\n 'cross_valid_ind': 1,\n 'data_path': 'dataset',\n 'data_url': '',\n 'dataset': 'kits19',\n 'device_target': 'Ascend',\n 'distribute_epochs': 2400,\n 'enable_modelarts': False,\n 'enable_profiling': False,\n 'epochs': 10,\n 'eval_activate': 'Softmax',\n 'eval_interval': 1,\n 'eval_metrics': 'dice_coeff',\n 'eval_resize': False,\n 'eval_start_epoch': 0,\n 'file_format': 'MINDIR',\n 'file_name': 'unet',\n 'filter_weight': ['final1.weight'],\n 'height': 512,\n 'image_size': [512, 512],\n 'include_background': False,\n 'keep_checkpoint_max': 10,\n 'load_path': './output/checkpoint_path/',\n 'loss_scale': 1024.0,\n 'lr': 0.0001,\n 'model_name': 'unet_simple',\n 'num_channels': 1,\n 'num_classes': 3,\n 'output_path': './output',\n 'pred_save_path': './prediction',\n 'raw_data_path': 'kits19',\n 'repeat': 1,\n 'result_path': './preprocess_Result',\n 'resume': False,\n 'resume_ckpt': './',\n 'rst_path': './result_Files/',\n 'run_distribute': False,\n 'run_eval': True,\n 'show_eval': False,\n 'split': 0.8,\n 'train_augment': True,\n 'train_url': '',\n 'transfer_training': False,\n 'weight_decay': 0.0005,\n 'width': 512}\nPlease check the above information for the configurations\n========== start preprocess kits19 dataset ==========\nimg_path kits19/case_00010/imaging.nii.gz image shape (512, 512, 50) type float64\nseg_path kits19/case_00010/segmentation.nii.gz seg shape (512, 512, 50) type uint8\nimg_path kits19/case_00007/imaging.nii.gz image shape (512, 512, 61) type float64\nimg_path kits19/case_00004/imaging.nii.gz image shape (512, 512, 64) type float64\nseg_path kits19/case_00007/segmentation.nii.gz seg shape (512, 512, 61) type uint8\nseg_path kits19/case_00004/segmentation.nii.gz seg shape (512, 512, 64) type uint8\nimg_path kits19/case_00015/imaging.nii.gz image shape (512, 512, 75) type float64\nseg_path kits19/case_00015/segmentation.nii.gz seg shape (512, 512, 75) type uint16\nimg_path kits19/case_00009/imaging.nii.gz image shape (512, 512, 77) type float64\nseg_path kits19/case_00009/segmentation.nii.gz seg shape (512, 512, 77) type uint8\nimg_path kits19/case_00011/imaging.nii.gz image shape (512, 512, 80) type float64\nseg_path kits19/case_00011/segmentation.nii.gz seg shape (512, 512, 80) type uint8\nimg_path kits19/case_00012/imaging.nii.gz image shape (512, 512, 89) type float64\nimg_path kits19/case_00013/imaging.nii.gz image shape (512, 512, 92) type float64\nseg_path kits19/case_00012/segmentation.nii.gz seg shape (512, 512, 89) type uint8\nseg_path kits19/case_00013/segmentation.nii.gz seg shape (512, 512, 92) type uint8\nimg_path kits19/case_00006/imaging.nii.gz image shape (512, 512, 157) type float64\nseg_path kits19/case_00006/segmentation.nii.gz seg shape (512, 512, 157) type uint8\nimg_path kits19/case_00002/imaging.nii.gz image shape (512, 512, 261) type float64\nimg_path kits19/case_00008/imaging.nii.gz image shape (512, 512, 227) type float64\nseg_path kits19/case_00002/segmentation.nii.gz seg shape (512, 512, 261) type uint8\nseg_path kits19/case_00008/segmentation.nii.gz seg shape (512, 512, 227) type uint8\nimg_path kits19/case_00003/imaging.nii.gz image shape (512, 512, 270) type float64\nseg_path kits19/case_00003/segmentation.nii.gz seg shape (512, 512, 270) type uint8\nfinale down_scale shape (512, 512, 25)\nimg_path removed kits19/case_00010/imaging.nii.gz\nseg_path removed kits19/case_00010/segmentation.nii.gz\nfinale down_scale shape (512, 512, 30)\nimg_path removed kits19/case_00007/imaging.nii.gz\nseg_path removed kits19/case_00007/segmentation.nii.gz\nfinale down_scale shape (512, 512, 32)\nimg_path removed kits19/case_00004/imaging.nii.gz\nseg_path removed kits19/case_00004/segmentation.nii.gz\nfinale down_scale shape (512, 512, 38)\nimg_path kits19/case_00017/imaging.nii.gz image shape (512, 512, 97) type float64\nfinale down_scale shape (512, 512, 38)\nseg_path kits19/case_00017/segmentation.nii.gz seg shape (512, 512, 97) type uint8\nimg_path removed kits19/case_00015/imaging.nii.gz\nseg_path removed kits19/case_00015/segmentation.nii.gz\nimg_path kits19/case_00016/imaging.nii.gz image shape (512, 512, 178) type float64\nseg_path kits19/case_00016/segmentation.nii.gz seg shape (512, 512, 178) type uint8\nimg_path removed kits19/case_00009/imaging.nii.gz\nseg_path removed kits19/case_00009/segmentation.nii.gz\nfinale down_scale shape (512, 512, 40)\nimg_path kits19/case_00018/imaging.nii.gz image shape (512, 512, 121) type float64\nseg_path kits19/case_00018/segmentation.nii.gz seg shape (512, 512, 121) type uint8\nimg_path removed kits19/case_00011/imaging.nii.gz\nseg_path removed kits19/case_00011/segmentation.nii.gz\nfinale down_scale shape (512, 512, 44)\nimg_path kits19/case_00020/imaging.nii.gz image shape (512, 512, 96) type float64\nimg_path kits19/case_00021/imaging.nii.gz image shape (512, 512, 38) type float64\nseg_path kits19/case_00020/segmentation.nii.gz seg shape (512, 512, 96) type uint8\nseg_path kits19/case_00021/segmentation.nii.gz seg shape (512, 512, 38) type uint8\nimg_path kits19/case_00019/imaging.nii.gz image shape (512, 512, 129) type float64\nfinale down_scale shape (512, 512, 46)\nseg_path kits19/case_00019/segmentation.nii.gz seg shape (512, 512, 129) type uint8\nimg_path removed kits19/case_00012/imaging.nii.gz\nseg_path removed kits19/case_00012/segmentation.nii.gz\nimg_path removed kits19/case_00013/imaging.nii.gz\nseg_path removed kits19/case_00013/segmentation.nii.gz\nimg_path kits19/case_00014/imaging.nii.gz image shape (512, 512, 439) type float64\nseg_path kits19/case_00014/segmentation.nii.gz seg shape (512, 512, 439) type uint8\nimg_path kits19/case_00000/imaging.nii.gz image shape (512, 512, 611) type float64\nimg_path kits19/case_00023/imaging.nii.gz image shape (512, 512, 107) type float64\nseg_path kits19/case_00023/segmentation.nii.gz seg shape (512, 512, 107) type uint16\nimg_path kits19/case_00005/imaging.nii.gz image shape (512, 512, 834) type float64\nseg_path kits19/case_00000/segmentation.nii.gz seg shape (512, 512, 611) type uint8\nfinale down_scale shape (512, 512, 19)\nimg_path kits19/case_00001/imaging.nii.gz image shape (512, 512, 602) type float64\nseg_path kits19/case_00005/segmentation.nii.gz seg shape (512, 512, 834) type uint8\nimg_path removed kits19/case_00021/imaging.nii.gz\nseg_path removed kits19/case_00021/segmentation.nii.gz\nseg_path kits19/case_00001/segmentation.nii.gz seg shape (512, 512, 602) type uint8\nimg_path kits19/case_00024/imaging.nii.gz image shape (512, 512, 85) type float64\nseg_path kits19/case_00024/segmentation.nii.gz seg shape (512, 512, 85) type uint8\nfinale down_scale shape (512, 512, 78)\nfinale down_scale shape (512, 512, 48)\nimg_path removed kits19/case_00017/imaging.nii.gz\nseg_path removed kits19/case_00017/segmentation.nii.gz\nimg_path removed kits19/case_00006/imaging.nii.gz\nseg_path removed kits19/case_00006/segmentation.nii.gz\nimg_path kits19/case_00025/imaging.nii.gz image shape (512, 512, 103) type float64\nseg_path kits19/case_00025/segmentation.nii.gz seg shape (512, 512, 103) type uint8\nfinale down_scale shape (512, 512, 48)\nimg_path kits19/case_00022/imaging.nii.gz image shape (512, 512, 541) type float64\nimg_path removed kits19/case_00020/imaging.nii.gz\nseg_path removed kits19/case_00020/segmentation.nii.gz\nfinale down_scale shape (512, 512, 60)\nseg_path kits19/case_00022/segmentation.nii.gz seg shape (512, 512, 541) type uint8\nimg_path removed kits19/case_00018/imaging.nii.gz\nseg_path removed kits19/case_00018/segmentation.nii.gz\nfinale down_scale shape (512, 512, 64)\nimg_path kits19/case_00026/imaging.nii.gz image shape (512, 512, 302) type float64\nimg_path kits19/case_00028/imaging.nii.gz image shape (512, 512, 98) type float64\nseg_path kits19/case_00026/segmentation.nii.gz seg shape (512, 512, 302) type uint8\nseg_path kits19/case_00028/segmentation.nii.gz seg shape (512, 512, 98) type uint8\nfinale down_scale shape (512, 512, 54)\nimg_path removed kits19/case_00019/imaging.nii.gz\nseg_path removed kits19/case_00019/segmentation.nii.gz\nimg_path removed kits19/case_00023/imaging.nii.gz\nseg_path removed kits19/case_00023/segmentation.nii.gz\nfinale down_scale shape (512, 512, 42)\nimg_path removed kits19/case_00024/imaging.nii.gz\nseg_path removed kits19/case_00024/segmentation.nii.gz\nimg_path kits19/case_00030/imaging.nii.gz image shape (512, 512, 38) type float64\nseg_path kits19/case_00030/segmentation.nii.gz seg shape (512, 512, 38) type uint8\nfinale down_scale shape (512, 512, 114)\nfinale down_scale shape (512, 512, 89)\nimg_path kits19/case_00029/imaging.nii.gz image shape (512, 512, 131) type float64\nseg_path kits19/case_00029/segmentation.nii.gz seg shape (512, 512, 131) type uint8\nimg_path removed kits19/case_00016/imaging.nii.gz\nseg_path removed kits19/case_00016/segmentation.nii.gz\nimg_path removed kits19/case_00008/imaging.nii.gz\nseg_path removed kits19/case_00008/segmentation.nii.gz\nimg_path kits19/case_00031/imaging.nii.gz image shape (512, 512, 117) type float64\nseg_path kits19/case_00031/segmentation.nii.gz seg shape (512, 512, 117) type uint8\nfinale down_scale shape (512, 512, 130)\nfinale down_scale shape (512, 512, 19)\nfinale down_scale shape (512, 512, 52)\nimg_path removed kits19/case_00030/imaging.nii.gz\nseg_path removed kits19/case_00030/segmentation.nii.gz\nimg_path kits19/case_00032/imaging.nii.gz image shape (512, 512, 189) type float64\nimg_path removed kits19/case_00025/imaging.nii.gz\nseg_path removed kits19/case_00025/segmentation.nii.gz\nseg_path kits19/case_00032/segmentation.nii.gz seg shape (512, 512, 189) type uint8\nfinale down_scale shape (512, 512, 135)\nimg_path removed kits19/case_00002/imaging.nii.gz\nseg_path removed kits19/case_00002/segmentation.nii.gz\nimg_path kits19/case_00034/imaging.nii.gz image shape (512, 512, 110) type float64\nseg_path kits19/case_00034/segmentation.nii.gz seg shape (512, 512, 110) type uint8\nimg_path kits19/case_00035/imaging.nii.gz image shape (512, 512, 98) type float64\nseg_path kits19/case_00035/segmentation.nii.gz seg shape (512, 512, 98) type uint8\nimg_path kits19/case_00027/imaging.nii.gz image shape (512, 512, 723) type float64\nfinale down_scale shape (512, 512, 49)\nimg_path removed kits19/case_00003/imaging.nii.gz\nseg_path removed kits19/case_00003/segmentation.nii.gz\nimg_path removed kits19/case_00028/imaging.nii.gz\nseg_path removed kits19/case_00028/segmentation.nii.gz\nseg_path kits19/case_00027/segmentation.nii.gz seg shape (512, 512, 723) type uint8\nimg_path kits19/case_00038/imaging.nii.gz image shape (512, 512, 32) type float64\nseg_path kits19/case_00038/segmentation.nii.gz seg shape (512, 512, 32) type uint8\nimg_path kits19/case_00036/imaging.nii.gz image shape (512, 512, 163) type float64\nseg_path kits19/case_00036/segmentation.nii.gz seg shape (512, 512, 163) type uint8\nimg_path kits19/case_00033/imaging.nii.gz image shape (512, 512, 423) type float64\nimg_path kits19/case_00037/imaging.nii.gz image shape (512, 512, 97) type float64\nseg_path kits19/case_00037/segmentation.nii.gz seg shape (512, 512, 97) type uint16\nseg_path kits19/case_00033/segmentation.nii.gz seg shape (512, 512, 423) type uint8\nfinale down_scale shape (512, 512, 16)\nimg_path removed kits19/case_00038/imaging.nii.gz\nseg_path removed kits19/case_00038/segmentation.nii.gz\nfinale down_scale shape (512, 512, 58)\nfinale down_scale shape (512, 512, 66)\nimg_path removed kits19/case_00031/imaging.nii.gz\nseg_path removed kits19/case_00031/segmentation.nii.gz\nimg_path kits19/case_00039/imaging.nii.gz image shape (512, 512, 90) type float64\nseg_path kits19/case_00039/segmentation.nii.gz seg shape (512, 512, 90) type uint16\nimg_path removed kits19/case_00029/imaging.nii.gz\nseg_path removed kits19/case_00029/segmentation.nii.gz\nimg_path kits19/case_00041/imaging.nii.gz image shape (512, 512, 52) type float64\nseg_path kits19/case_00041/segmentation.nii.gz seg shape (512, 512, 52) type uint8\nfinale down_scale shape (512, 512, 49)\nimg_path removed kits19/case_00035/imaging.nii.gz\nseg_path removed kits19/case_00035/segmentation.nii.gz\nfinale down_scale shape (512, 512, 55)\nimg_path removed kits19/case_00034/imaging.nii.gz\nseg_path removed kits19/case_00034/segmentation.nii.gz\nimg_path kits19/case_00040/imaging.nii.gz image shape (512, 512, 207) type float64\nseg_path kits19/case_00040/segmentation.nii.gz seg shape (512, 512, 207) type uint8\nfinale down_scale shape (512, 512, 48)\nimg_path removed kits19/case_00037/imaging.nii.gz\nseg_path removed kits19/case_00037/segmentation.nii.gz\nimg_path kits19/case_00043/imaging.nii.gz image shape (512, 512, 172) type float64\nseg_path kits19/case_00043/segmentation.nii.gz seg shape (512, 512, 172) type uint8\nfinale down_scale shape (512, 512, 26)\nimg_path removed kits19/case_00041/imaging.nii.gz\nseg_path removed kits19/case_00041/segmentation.nii.gz\nimg_path kits19/case_00044/imaging.nii.gz image shape (512, 512, 101) type float64\nimg_path kits19/case_00042/imaging.nii.gz image shape (512, 512, 301) type float64\nseg_path kits19/case_00044/segmentation.nii.gz seg shape (512, 512, 101) type uint8\nimg_path kits19/case_00045/imaging.nii.gz image shape (512, 512, 62) type float64\nseg_path kits19/case_00042/segmentation.nii.gz seg shape (512, 512, 301) type uint8\nseg_path kits19/case_00045/segmentation.nii.gz seg shape (512, 512, 62) type uint8\nfinale down_scale shape (512, 512, 45)\nfinale down_scale shape (512, 512, 94)\nimg_path removed kits19/case_00039/imaging.nii.gz\nseg_path removed kits19/case_00039/segmentation.nii.gz\nimg_path removed kits19/case_00032/imaging.nii.gz\nseg_path removed kits19/case_00032/segmentation.nii.gz\nfinale down_scale shape (512, 512, 82)\nimg_path kits19/case_00046/imaging.nii.gz image shape (512, 512, 159) type float64\nimg_path removed kits19/case_00036/imaging.nii.gz\nseg_path removed kits19/case_00036/segmentation.nii.gz\nseg_path kits19/case_00046/segmentation.nii.gz seg shape (512, 512, 159) type uint8\nimg_path kits19/case_00047/imaging.nii.gz image shape (512, 512, 142) type float64\nseg_path kits19/case_00047/segmentation.nii.gz seg shape (512, 512, 142) type uint8\nimg_path kits19/case_00048/imaging.nii.gz image shape (512, 512, 85) type float64\nseg_path kits19/case_00048/segmentation.nii.gz seg shape (512, 512, 85) type uint8\nfinale down_scale shape (512, 512, 151)\nfinale down_scale shape (512, 512, 31)\nimg_path removed kits19/case_00045/imaging.nii.gz\nseg_path removed kits19/case_00045/segmentation.nii.gz\nimg_path removed kits19/case_00026/imaging.nii.gz\nseg_path removed kits19/case_00026/segmentation.nii.gz\nfinale down_scale shape (512, 512, 50)\nimg_path kits19/case_00050/imaging.nii.gz image shape (512, 512, 96) type float64\nseg_path kits19/case_00050/segmentation.nii.gz seg shape (512, 512, 96) type uint8\nimg_path removed kits19/case_00044/imaging.nii.gz\nseg_path removed kits19/case_00044/segmentation.nii.gz\nfinale down_scale shape (512, 512, 220)\nimg_path kits19/case_00051/imaging.nii.gz image shape (512, 512, 68) type float64\nseg_path kits19/case_00051/segmentation.nii.gz seg shape (512, 512, 68) type uint8\nfinale down_scale shape (512, 512, 42)\nimg_path removed kits19/case_00014/imaging.nii.gz\nseg_path removed kits19/case_00014/segmentation.nii.gz\nimg_path removed kits19/case_00048/imaging.nii.gz\nseg_path removed kits19/case_00048/segmentation.nii.gz\nfinale down_scale shape (512, 512, 86)\nfinale down_scale shape (512, 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kits19/case_00135/imaging.nii.gz\nseg_path removed kits19/case_00135/segmentation.nii.gz\nfinale down_scale shape (512, 512, 235)\nfinale down_scale shape (512, 512, 46)\nimg_path kits19/case_00174/imaging.nii.gz image shape (512, 512, 69) type float64\nseg_path kits19/case_00174/segmentation.nii.gz seg shape (512, 512, 69) type uint8\nimg_path removed kits19/case_00172/imaging.nii.gz\nseg_path removed kits19/case_00172/segmentation.nii.gz\nimg_path removed kits19/case_00160/imaging.nii.gz\nseg_path removed kits19/case_00160/segmentation.nii.gz\nimg_path kits19/case_00175/imaging.nii.gz image shape (512, 512, 107) type float64\nfinale down_scale shape (512, 512, 290)\nseg_path kits19/case_00175/segmentation.nii.gz seg shape (512, 512, 107) type uint8\nimg_path kits19/case_00176/imaging.nii.gz image shape (512, 512, 102) type float64\nimg_path removed kits19/case_00154/imaging.nii.gz\nseg_path removed kits19/case_00154/segmentation.nii.gz\nfinale down_scale shape (512, 512, 66)\nseg_path kits19/case_00176/segmentation.nii.gz seg shape (512, 512, 102) type uint16\nimg_path removed kits19/case_00171/imaging.nii.gz\nseg_path removed kits19/case_00171/segmentation.nii.gz\nfinale down_scale shape (512, 512, 296)\nimg_path kits19/case_00177/imaging.nii.gz image shape (512, 512, 88) type float64\nseg_path kits19/case_00177/segmentation.nii.gz seg shape (512, 512, 88) type uint8\nimg_path kits19/case_00178/imaging.nii.gz image shape (512, 512, 88) type float64\nseg_path kits19/case_00178/segmentation.nii.gz seg shape (512, 512, 88) type uint8\nfinale down_scale shape (512, 512, 48)\nfinale down_scale shape (512, 512, 34)\nimg_path removed kits19/case_00173/imaging.nii.gz\nseg_path removed kits19/case_00173/segmentation.nii.gz\nimg_path removed kits19/case_00174/imaging.nii.gz\nseg_path removed kits19/case_00174/segmentation.nii.gz\nimg_path removed kits19/case_00141/imaging.nii.gz\nseg_path removed kits19/case_00141/segmentation.nii.gz\nfinale down_scale shape (512, 512, 269)\nimg_path kits19/case_00179/imaging.nii.gz image shape (512, 512, 99) type float64\nseg_path kits19/case_00179/segmentation.nii.gz seg shape (512, 512, 99) type uint8\nimg_path kits19/case_00180/imaging.nii.gz image shape (512, 512, 137) type float64\nseg_path kits19/case_00180/segmentation.nii.gz seg shape (512, 512, 137) type uint8\nimg_path kits19/case_00181/imaging.nii.gz image shape (512, 512, 99) type float64\nseg_path kits19/case_00181/segmentation.nii.gz seg shape (512, 512, 99) type uint8\nimg_path removed kits19/case_00146/imaging.nii.gz\nseg_path removed kits19/case_00146/segmentation.nii.gz\nimg_path kits19/case_00182/imaging.nii.gz image shape (512, 512, 93) type float64\nseg_path kits19/case_00182/segmentation.nii.gz seg shape (512, 512, 93) type uint8\nfinale down_scale shape (512, 512, 54)\nimg_path removed kits19/case_00175/imaging.nii.gz\nseg_path removed kits19/case_00175/segmentation.nii.gz\nimg_path removed kits19/case_00155/imaging.nii.gz\nseg_path removed kits19/case_00155/segmentation.nii.gz\nfinale down_scale shape (512, 512, 51)\nfinale down_scale shape (512, 512, 274)\nfinale down_scale shape (512, 512, 44)\nimg_path removed kits19/case_00176/imaging.nii.gz\nseg_path removed kits19/case_00176/segmentation.nii.gz\nfinale down_scale shape (512, 512, 44)\nimg_path removed kits19/case_00177/imaging.nii.gz\nseg_path removed kits19/case_00177/segmentation.nii.gz\nimg_path removed kits19/case_00178/imaging.nii.gz\nseg_path removed kits19/case_00178/segmentation.nii.gz\nimg_path kits19/case_00187/imaging.nii.gz image shape (512, 512, 82) type float64\nseg_path kits19/case_00187/segmentation.nii.gz seg shape (512, 512, 82) type uint8\nimg_path kits19/case_00184/imaging.nii.gz image shape (512, 512, 146) type float64\nseg_path kits19/case_00184/segmentation.nii.gz seg shape (512, 512, 146) type uint8\nimg_path kits19/case_00183/imaging.nii.gz image shape (512, 512, 195) type float64\nseg_path kits19/case_00183/segmentation.nii.gz seg shape (512, 512, 195) type uint8\nimg_path kits19/case_00186/imaging.nii.gz image shape (512, 512, 143) type float64\nseg_path kits19/case_00186/segmentation.nii.gz seg shape (512, 512, 143) type uint8\nfinale down_scale shape (512, 512, 50)\nimg_path kits19/case_00185/imaging.nii.gz image shape (512, 512, 235) type float64\nimg_path removed kits19/case_00179/imaging.nii.gz\nseg_path removed kits19/case_00179/segmentation.nii.gz\nseg_path kits19/case_00185/segmentation.nii.gz seg shape (512, 512, 235) type uint8\nimg_path removed kits19/case_00157/imaging.nii.gz\nseg_path removed kits19/case_00157/segmentation.nii.gz\nfinale down_scale shape (512, 512, 50)\nimg_path removed kits19/case_00181/imaging.nii.gz\nseg_path removed kits19/case_00181/segmentation.nii.gz\nfinale down_scale shape (512, 512, 46)\nimg_path removed kits19/case_00182/imaging.nii.gz\nseg_path removed kits19/case_00182/segmentation.nii.gz\nimg_path kits19/case_00189/imaging.nii.gz image shape (512, 512, 146) type float64\nseg_path kits19/case_00189/segmentation.nii.gz seg shape (512, 512, 146) type uint8\nfinale down_scale shape (512, 512, 68)\nimg_path kits19/case_00190/imaging.nii.gz image shape (512, 512, 161) type float64\nseg_path kits19/case_00190/segmentation.nii.gz seg shape (512, 512, 161) type uint8\nimg_path removed kits19/case_00180/imaging.nii.gz\nseg_path removed kits19/case_00180/segmentation.nii.gz\nfinale down_scale shape (512, 512, 41)\nimg_path removed kits19/case_00187/imaging.nii.gz\nseg_path removed kits19/case_00187/segmentation.nii.gz\nimg_path kits19/case_00188/imaging.nii.gz image shape (512, 512, 365) type float64\nseg_path kits19/case_00188/segmentation.nii.gz seg shape (512, 512, 365) type uint8\nimg_path kits19/case_00192/imaging.nii.gz image shape (512, 512, 133) type float64\nseg_path kits19/case_00192/segmentation.nii.gz seg shape (512, 512, 133) type uint8\nfinale down_scale shape (512, 512, 172)\nimg_path kits19/case_00191/imaging.nii.gz image shape (512, 512, 349) type float64\nseg_path kits19/case_00191/segmentation.nii.gz seg shape (512, 512, 349) type uint8\nimg_path kits19/case_00193/imaging.nii.gz image shape (512, 512, 233) type float64\nseg_path kits19/case_00193/segmentation.nii.gz seg shape (512, 512, 233) type uint8\nimg_path removed kits19/case_00170/imaging.nii.gz\nseg_path removed kits19/case_00170/segmentation.nii.gz\nfinale down_scale shape (512, 512, 73)\nimg_path removed kits19/case_00184/imaging.nii.gz\nseg_path removed kits19/case_00184/segmentation.nii.gz\nfinale down_scale shape (512, 512, 72)\nimg_path kits19/case_00194/imaging.nii.gz image shape (512, 512, 135) type float64\nseg_path kits19/case_00194/segmentation.nii.gz seg shape (512, 512, 135) type uint8\nimg_path removed kits19/case_00186/imaging.nii.gz\nseg_path removed kits19/case_00186/segmentation.nii.gz\nimg_path kits19/case_00195/imaging.nii.gz image shape (512, 512, 98) type float64\nseg_path kits19/case_00195/segmentation.nii.gz seg shape (512, 512, 98) type uint8\nimg_path kits19/case_00196/imaging.nii.gz image shape (512, 512, 178) type float64\nfinale down_scale shape (512, 512, 352)\nseg_path kits19/case_00196/segmentation.nii.gz seg shape (512, 512, 178) type uint8\nfinale down_scale shape (512, 512, 73)\nfinale down_scale shape (512, 512, 98)\nimg_path removed kits19/case_00189/imaging.nii.gz\nseg_path removed kits19/case_00189/segmentation.nii.gz\nimg_path removed kits19/case_00183/imaging.nii.gz\nseg_path removed kits19/case_00183/segmentation.nii.gz\nfinale down_scale shape (512, 512, 66)\nfinale down_scale shape (512, 512, 80)\nfinale down_scale shape (512, 512, 360)\nimg_path removed kits19/case_00192/imaging.nii.gz\nseg_path removed kits19/case_00192/segmentation.nii.gz\nimg_path removed kits19/case_00190/imaging.nii.gz\nseg_path removed kits19/case_00190/segmentation.nii.gz\nimg_path kits19/case_00197/imaging.nii.gz image shape (512, 512, 162) type float64\nseg_path kits19/case_00197/segmentation.nii.gz seg shape (512, 512, 162) type uint8\nfinale down_scale shape (512, 512, 118)\nimg_path kits19/case_00199/imaging.nii.gz image shape (512, 512, 121) type float64\nseg_path kits19/case_00199/segmentation.nii.gz seg shape (512, 512, 121) type uint8\nimg_path kits19/case_00200/imaging.nii.gz image shape (512, 512, 103) type float64\nseg_path kits19/case_00200/segmentation.nii.gz seg shape (512, 512, 103) type uint8\nimg_path removed kits19/case_00158/imaging.nii.gz\nseg_path removed kits19/case_00158/segmentation.nii.gz\nfinale down_scale shape (512, 512, 49)\nimg_path removed kits19/case_00185/imaging.nii.gz\nseg_path removed kits19/case_00185/segmentation.nii.gz\nimg_path removed kits19/case_00195/imaging.nii.gz\nseg_path removed kits19/case_00195/segmentation.nii.gz\nimg_path kits19/case_00198/imaging.nii.gz image shape (512, 512, 269) type float64\nseg_path kits19/case_00198/segmentation.nii.gz seg shape (512, 512, 269) type uint8\nimg_path kits19/case_00201/imaging.nii.gz image shape (512, 512, 96) type float64\nseg_path kits19/case_00201/segmentation.nii.gz seg shape (512, 512, 96) type uint8\nfinale down_scale shape (512, 512, 68)\nimg_path removed kits19/case_00159/imaging.nii.gz\nseg_path removed kits19/case_00159/segmentation.nii.gz\nimg_path removed kits19/case_00194/imaging.nii.gz\nseg_path removed kits19/case_00194/segmentation.nii.gz\nimg_path kits19/case_00204/imaging.nii.gz image shape (512, 512, 75) type float64\nseg_path kits19/case_00204/segmentation.nii.gz seg shape (512, 512, 75) type uint8\nimg_path kits19/case_00205/imaging.nii.gz image shape (512, 512, 93) type float64\nseg_path kits19/case_00205/segmentation.nii.gz seg shape (512, 512, 93) type uint8\nimg_path kits19/case_00202/imaging.nii.gz image shape (512, 512, 383) type float64\nseg_path kits19/case_00202/segmentation.nii.gz seg shape (512, 512, 383) type uint8\nfinale down_scale shape (512, 512, 116)\nfinale down_scale shape (512, 512, 52)\nimg_path removed kits19/case_00200/imaging.nii.gz\nseg_path removed kits19/case_00200/segmentation.nii.gz\nfinale down_scale shape (512, 512, 89)\nfinale down_scale shape (512, 512, 60)\nimg_path removed kits19/case_00193/imaging.nii.gz\nseg_path removed kits19/case_00193/segmentation.nii.gz\nimg_path kits19/case_00206/imaging.nii.gz image shape (512, 512, 60) type float64\nseg_path kits19/case_00206/segmentation.nii.gz seg shape (512, 512, 60) type uint8\nfinale down_scale shape (512, 512, 48)\nimg_path removed kits19/case_00196/imaging.nii.gz\nseg_path removed kits19/case_00196/segmentation.nii.gz\nimg_path removed kits19/case_00199/imaging.nii.gz\nseg_path removed kits19/case_00199/segmentation.nii.gz\nimg_path kits19/case_00203/imaging.nii.gz image shape (512, 512, 620) type float64\nfinale down_scale shape (512, 512, 38)\nimg_path removed kits19/case_00201/imaging.nii.gz\nseg_path removed kits19/case_00201/segmentation.nii.gz\nseg_path kits19/case_00203/segmentation.nii.gz seg shape (512, 512, 620) type uint8\nfinale down_scale shape (512, 512, 367)\nimg_path removed kits19/case_00204/imaging.nii.gz\nseg_path removed kits19/case_00204/segmentation.nii.gz\nimg_path kits19/case_00208/imaging.nii.gz image shape (512, 512, 89) type float64\nseg_path kits19/case_00208/segmentation.nii.gz seg shape (512, 512, 89) type uint8\nimg_path kits19/case_00207/imaging.nii.gz image shape (512, 512, 140) type float64\nfinale down_scale shape (512, 512, 81)\nimg_path kits19/case_00209/imaging.nii.gz image shape (512, 512, 102) type float64\nseg_path kits19/case_00207/segmentation.nii.gz seg shape (512, 512, 140) type uint8\nseg_path kits19/case_00209/segmentation.nii.gz seg shape (512, 512, 102) type uint8\nfinale down_scale shape (512, 512, 46)\nimg_path removed kits19/case_00197/imaging.nii.gz\nseg_path removed kits19/case_00197/segmentation.nii.gz\nimg_path removed kits19/case_00205/imaging.nii.gz\nseg_path removed kits19/case_00205/segmentation.nii.gz\nfinale down_scale shape (512, 512, 30)\nimg_path removed kits19/case_00165/imaging.nii.gz\nseg_path removed kits19/case_00165/segmentation.nii.gz\nimg_path removed kits19/case_00206/imaging.nii.gz\nseg_path removed kits19/case_00206/segmentation.nii.gz\nfinale down_scale shape (512, 512, 494)\nfinale down_scale shape (512, 512, 182)\nfinale down_scale shape (512, 512, 174)\nimg_path removed kits19/case_00188/imaging.nii.gz\nseg_path removed kits19/case_00188/segmentation.nii.gz\nfinale down_scale shape (512, 512, 44)\nimg_path removed kits19/case_00191/imaging.nii.gz\nseg_path removed kits19/case_00191/segmentation.nii.gz\nimg_path removed kits19/case_00208/imaging.nii.gz\nseg_path removed kits19/case_00208/segmentation.nii.gz\nfinale down_scale shape (512, 512, 51)\nimg_path removed kits19/case_00209/imaging.nii.gz\nseg_path removed kits19/case_00209/segmentation.nii.gz\nimg_path removed kits19/case_00156/imaging.nii.gz\nseg_path removed kits19/case_00156/segmentation.nii.gz\nfinale down_scale shape (512, 512, 134)\nfinale down_scale shape (512, 512, 70)\nfinale down_scale shape (512, 512, 530)\nimg_path removed kits19/case_00207/imaging.nii.gz\nseg_path removed kits19/case_00207/segmentation.nii.gz\nimg_path removed kits19/case_00198/imaging.nii.gz\nseg_path removed kits19/case_00198/segmentation.nii.gz\nimg_path removed kits19/case_00151/imaging.nii.gz\nseg_path removed kits19/case_00151/segmentation.nii.gz\nfinale down_scale shape (512, 512, 192)\nimg_path removed kits19/case_00202/imaging.nii.gz\nseg_path removed kits19/case_00202/segmentation.nii.gz\nfinale down_scale shape (512, 512, 310)\nimg_path removed kits19/case_00203/imaging.nii.gz\nseg_path removed kits19/case_00203/segmentation.nii.gz\n========== end preprocess dataset ==========\n", "output_type": "stream"}]}, {"cell_type": "code", "source": "!python train.py --data_path=dataset --config_path=unet_simple_config.yaml --device_target=Ascend --batch_size=16 --epochs=50", "metadata": {"trusted": true}, "execution_count": 10, "outputs": [{"name": "stdout", "text": "{'enable_modelarts': 'Whether training on modelarts, default: False', 'data_url': 'Dataset url for obs', 'train_url': 'Training output url for obs', 'checkpoint_url': 'The location of checkpoint for obs', 'data_path': 'Dataset path for local', 'output_path': 'Training output path for local', 'load_path': 'The location of checkpoint for obs', 'device_target': 'Target device type, available: [Ascend, GPU, CPU]', 'enable_profiling': 'Whether enable profiling while training, default: False', 'num_classes': 'Class for dataset', 'batch_size': 'Batch size for training and evaluation', 'weight_decay': 'Weight decay.', 'keep_checkpoint_max': 'keep the last keep_checkpoint_max checkpoint', 'checkpoint_path': 'The location of the checkpoint file.', 'checkpoint_file_path': 'The location of the checkpoint file.', 'train_augment': 'Whether apply data augment when training.'}\n{'FixedLossScaleManager': 1024.0,\n 'batch_size': 16,\n 'checkpoint_file_path': 'ckpt_unet_simple_adam-4-75.ckpt',\n 'checkpoint_path': './checkpoint/',\n 'checkpoint_url': '',\n 'color': [[0, 0, 0],\n           [255, 0, 0],\n           [0, 255, 0],\n           [0, 0, 255],\n           [0, 255, 255],\n           [255, 0, 255],\n           [255, 255, 255]],\n 'config_path': 'unet_simple_config.yaml',\n 'crop': 'None',\n 'cross_valid_ind': 1,\n 'data_path': 'dataset',\n 'data_url': '',\n 'dataset': 'kits19',\n 'device_target': 'Ascend',\n 'distribute_epochs': 2400,\n 'enable_modelarts': False,\n 'enable_profiling': False,\n 'epochs': 50,\n 'eval_activate': 'Softmax',\n 'eval_interval': 1,\n 'eval_metrics': 'dice_coeff',\n 'eval_resize': False,\n 'eval_start_epoch': 0,\n 'file_format': 'MINDIR',\n 'file_name': 'unet',\n 'filter_weight': ['final1.weight'],\n 'height': 512,\n 'image_size': [512, 512],\n 'include_background': False,\n 'keep_checkpoint_max': 10,\n 'load_path': './output/checkpoint_path/',\n 'loss_scale': 1024.0,\n 'lr': 0.0001,\n 'model_name': 'unet_simple',\n 'num_channels': 1,\n 'num_classes': 3,\n 'output_path': './output',\n 'pred_save_path': './prediction',\n 'raw_data_path': './kits19',\n 'repeat': 1,\n 'result_path': './preprocess_Result',\n 'resume': False,\n 'resume_ckpt': './',\n 'rst_path': './result_Files/',\n 'run_distribute': False,\n 'run_eval': True,\n 'show_eval': False,\n 'split': 0.8,\n 'train_augment': True,\n 'train_url': '',\n 'transfer_training': False,\n 'weight_decay': 0.0005,\n 'width': 512}\nPlease check the above information for the configurations\n---using dataset  kits19\nforeground:  8101\nbackground:  2712\nforeground:  8101\nbackground:  2712\ndataset length is: 540\n============== Starting Training ==============\n[WARNING] SESSION(3439,ffff0cff9160,python):2022-10-17-03:22:20.631.640 [mindspore/ccsrc/backend/session/ascend_session.cc:1377] SelectKernel] There are 23 node/nodes used raise precision to selected the kernel!\nepoch:   1, avg loss:0.0444, total cost: 212.895 s, per step fps:40.583\n[WARNING] SESSION(3439,ffff0cff9160,python):2022-10-17-03:25:33.204.822 [mindspore/ccsrc/backend/session/ascend_session.cc:1377] SelectKernel] There are 10 node/nodes used raise precision to selected the kernel!\nepoch: 1, dice_coeff: 0.29692373907122543\nupdate best result: 0.29692373907122543\nupdate best checkpoint at: ./output/./checkpoint/ckpt_0/best.ckpt\nepoch:   2, avg loss:0.0540, total cost: 121.971 s, per step fps:70.837\nepoch: 2, dice_coeff: 0.4938239101293372\nupdate best result: 0.4938239101293372\nupdate best checkpoint at: ./output/./checkpoint/ckpt_0/best.ckpt\nepoch:   3, avg loss:0.0208, total cost: 122.445 s, per step fps:70.562\nepoch: 3, dice_coeff: 0.5921303078148166\nupdate best result: 0.5921303078148166\nupdate best checkpoint at: ./output/./checkpoint/ckpt_0/best.ckpt\nepoch:   4, avg loss:0.0372, total cost: 122.211 s, per step fps:70.697\nepoch: 4, dice_coeff: 0.5483126199878522\nepoch:   5, avg loss:0.0249, total cost: 125.443 s, per step fps:68.876\nepoch: 5, dice_coeff: 0.6297630698369059\nupdate best result: 0.6297630698369059\nupdate best checkpoint at: ./output/./checkpoint/ckpt_0/best.ckpt\nepoch:   6, avg loss:0.0303, total cost: 122.257 s, per step fps:70.671\nepoch: 6, dice_coeff: 0.6056353685206978\nepoch:   7, avg loss:0.0231, total cost: 126.743 s, per step fps:68.170\nepoch: 7, dice_coeff: 0.6523661565774965\nupdate best result: 0.6523661565774965\nupdate best checkpoint at: ./output/./checkpoint/ckpt_0/best.ckpt\nepoch:   8, avg loss:0.0098, total cost: 122.305 s, per step fps:70.643\nepoch: 8, dice_coeff: 0.7199992433047978\nupdate best result: 0.7199992433047978\nupdate best checkpoint at: ./output/./checkpoint/ckpt_0/best.ckpt\nepoch:   9, avg loss:0.0197, total cost: 122.748 s, per step fps:70.388\nepoch: 9, dice_coeff: 0.7054355383313498\nepoch:  10, avg loss:0.0349, total cost: 124.781 s, per step fps:69.241\nepoch: 10, dice_coeff: 0.7519195941392417\nupdate best result: 0.7519195941392417\nupdate best checkpoint at: ./output/./checkpoint/ckpt_0/best.ckpt\nepoch:  11, avg loss:0.0417, total cost: 123.350 s, per step fps:70.045\nepoch: 11, dice_coeff: 0.7217629606321749\nepoch:  12, avg loss:0.0435, total cost: 122.360 s, per step fps:70.612\nepoch: 12, dice_coeff: 0.741704745359954\nepoch:  13, avg loss:0.0225, total cost: 123.488 s, per step fps:69.966\nepoch: 13, dice_coeff: 0.7034253336610956\nepoch:  14, avg loss:0.0350, total cost: 124.357 s, per step fps:69.477\nepoch: 14, dice_coeff: 0.747059840203605\nepoch:  15, avg loss:0.0320, total cost: 127.176 s, per step fps:67.937\nepoch: 15, dice_coeff: 0.682629639088109\nepoch:  16, avg loss:0.0131, total cost: 122.080 s, per step fps:70.773\nepoch: 16, dice_coeff: 0.7602092506289\nupdate best result: 0.7602092506289\nupdate best checkpoint at: ./output/./checkpoint/ckpt_0/best.ckpt\nepoch:  17, avg loss:0.0270, total cost: 122.961 s, per step fps:70.266\nepoch: 17, dice_coeff: 0.764082699764326\nupdate best result: 0.764082699764326\nupdate best checkpoint at: ./output/./checkpoint/ckpt_0/best.ckpt\nepoch:  18, avg loss:0.0200, total cost: 127.707 s, per step fps:67.655\nepoch: 18, dice_coeff: 0.7297466813764619\nepoch:  19, avg loss:0.0154, total cost: 123.169 s, per step fps:70.147\nepoch: 19, dice_coeff: 0.7632918415419674\nepoch:  20, avg loss:0.0139, total cost: 123.236 s, per step fps:70.109\nepoch: 20, dice_coeff: 0.7325739291297324\nepoch:  21, avg loss:0.0183, total cost: 123.542 s, per step fps:69.936\nepoch: 21, dice_coeff: 0.7455317877599934\nepoch:  22, avg loss:0.0165, total cost: 123.792 s, per step fps:69.795\nepoch: 22, dice_coeff: 0.6995378485772784\nepoch:  23, avg loss:0.0212, total cost: 127.335 s, per step fps:67.852\nepoch: 23, dice_coeff: 0.7966283937746057\nupdate best result: 0.7966283937746057\nupdate best checkpoint at: ./output/./checkpoint/ckpt_0/best.ckpt\nepoch:  24, avg loss:0.0152, total cost: 123.063 s, per step fps:70.208\nepoch: 24, dice_coeff: 0.7824641701702147\nepoch:  25, avg loss:0.0171, total cost: 123.463 s, per step fps:69.980\nepoch: 25, dice_coeff: 0.7294589960073081\nepoch:  26, avg loss:0.0151, total cost: 126.215 s, per step fps:68.454\nepoch: 26, dice_coeff: 0.762617719607044\nepoch:  27, avg loss:0.0105, total cost: 126.154 s, per step fps:68.488\nepoch: 27, dice_coeff: 0.6744940688879235\nepoch:  28, avg loss:0.0110, total cost: 126.349 s, per step fps:68.382\nepoch: 28, dice_coeff: 0.7566033174314206\nepoch:  29, avg loss:0.0358, total cost: 126.039 s, per step fps:68.550\nepoch: 29, dice_coeff: 0.7833176310143649\nepoch:  30, avg loss:0.0331, total cost: 125.205 s, per step fps:69.007\nepoch: 30, dice_coeff: 0.7604165192450402\nepoch:  31, avg loss:0.0216, total cost: 130.709 s, per step fps:66.101\nepoch: 31, dice_coeff: 0.7086771307175775\nepoch:  32, avg loss:0.0116, total cost: 128.424 s, per step fps:67.277\nepoch: 32, dice_coeff: 0.7791175027959074\nepoch:  33, avg loss:0.0130, total cost: 125.530 s, per step fps:68.828\nepoch: 33, dice_coeff: 0.7449107697754291\nepoch:  34, avg loss:0.0122, total cost: 124.321 s, per step fps:69.497\nepoch: 34, dice_coeff: 0.7892870495025106\nepoch:  35, avg loss:0.0171, total cost: 125.648 s, per step fps:68.763\nepoch: 35, dice_coeff: 0.7746093616555151\nepoch:  36, avg loss:0.0093, total cost: 126.234 s, per step fps:68.444\nepoch: 36, dice_coeff: 0.7305852836432155\nepoch:  37, avg loss:0.0225, total cost: 127.382 s, per step fps:67.827\nepoch: 37, dice_coeff: 0.7837852144772149\nepoch:  38, avg loss:0.0175, total cost: 123.934 s, per step fps:69.715\nepoch: 38, dice_coeff: 0.5110306251472055\nepoch:  39, avg loss:0.0184, total cost: 125.771 s, per step fps:68.696\nepoch: 39, dice_coeff: 0.772889105844272\nepoch:  40, avg loss:0.0098, total cost: 124.490 s, per step fps:69.403\nepoch: 40, dice_coeff: 0.784495175440839\nepoch:  41, avg loss:0.0118, total cost: 125.464 s, per step fps:68.864\nepoch: 41, dice_coeff: 0.7303237160615489\nepoch:  42, avg loss:0.0294, total cost: 126.801 s, per step fps:68.138\nepoch: 42, dice_coeff: 0.7563091651825851\nepoch:  43, avg loss:0.0064, total cost: 125.592 s, per step fps:68.794\nepoch: 43, dice_coeff: 0.7826399594309289\nepoch:  44, avg loss:0.0264, total cost: 123.434 s, per step fps:69.997\nepoch: 44, dice_coeff: 0.8040116783042911\nupdate best result: 0.8040116783042911\nupdate best checkpoint at: ./output/./checkpoint/ckpt_0/best.ckpt\nepoch:  45, avg loss:0.0164, total cost: 127.249 s, per step fps:67.898\nepoch: 45, dice_coeff: 0.7705114052448844\nepoch:  46, avg loss:0.0108, total cost: 124.278 s, per step fps:69.521\nepoch: 46, dice_coeff: 0.7437274643443567\nepoch:  47, avg loss:0.0104, total cost: 124.875 s, per step fps:69.189\nepoch: 47, dice_coeff: 0.7857733958603076\nepoch:  48, avg loss:0.0143, total cost: 126.277 s, per step fps:68.421\nepoch: 48, dice_coeff: 0.7278920157474384\nepoch:  49, avg loss:0.0136, total cost: 124.994 s, per step fps:69.123\nepoch: 49, dice_coeff: 0.7496601993607925\nepoch:  50, avg loss:0.0073, total cost: 123.830 s, per step fps:69.773\nepoch: 50, dice_coeff: 0.7226898169968129\nEnd training, the best dice_coeff is: 0.8040116783042911, the best dice_coeff epoch is 44\n============== End Training ==============\n\n", "output_type": "stream"}]}, {"cell_type": "code", "source": "!python eval.py --data_path=dataset --config_path=unet_simple_config.yaml --checkpoint_file_path=output/checkpoint/ckpt_0/best.ckpt --device_target=Ascend", "metadata": {"trusted": true}, "execution_count": 11, "outputs": [{"name": "stdout", "text": "{'enable_modelarts': 'Whether training on modelarts, default: False', 'data_url': 'Dataset url for obs', 'train_url': 'Training output url for obs', 'checkpoint_url': 'The location of checkpoint for obs', 'data_path': 'Dataset path for local', 'output_path': 'Training output path for local', 'load_path': 'The location of checkpoint for obs', 'device_target': 'Target device type, available: [Ascend, GPU, CPU]', 'enable_profiling': 'Whether enable profiling while training, default: False', 'num_classes': 'Class for dataset', 'batch_size': 'Batch size for training and evaluation', 'weight_decay': 'Weight decay.', 'keep_checkpoint_max': 'keep the last keep_checkpoint_max checkpoint', 'checkpoint_path': 'The location of the checkpoint file.', 'checkpoint_file_path': 'The location of the checkpoint file.', 'train_augment': 'Whether apply data augment when training.'}\n{'FixedLossScaleManager': 1024.0,\n 'batch_size': 16,\n 'checkpoint_file_path': 'output/checkpoint/ckpt_0/best.ckpt',\n 'checkpoint_path': './checkpoint/',\n 'checkpoint_url': '',\n 'color': [[0, 0, 0],\n           [255, 0, 0],\n           [0, 255, 0],\n           [0, 0, 255],\n           [0, 255, 255],\n           [255, 0, 255],\n           [255, 255, 255]],\n 'config_path': 'unet_simple_config.yaml',\n 'crop': 'None',\n 'cross_valid_ind': 1,\n 'data_path': 'dataset',\n 'data_url': '',\n 'dataset': 'kits19',\n 'device_target': 'Ascend',\n 'distribute_epochs': 2400,\n 'enable_modelarts': False,\n 'enable_profiling': False,\n 'epochs': 10,\n 'eval_activate': 'Softmax',\n 'eval_interval': 1,\n 'eval_metrics': 'dice_coeff',\n 'eval_resize': False,\n 'eval_start_epoch': 0,\n 'file_format': 'MINDIR',\n 'file_name': 'unet',\n 'filter_weight': ['final1.weight'],\n 'height': 512,\n 'image_size': [512, 512],\n 'include_background': False,\n 'keep_checkpoint_max': 10,\n 'load_path': './output/checkpoint_path/',\n 'loss_scale': 1024.0,\n 'lr': 0.0001,\n 'model_name': 'unet_simple',\n 'num_channels': 1,\n 'num_classes': 3,\n 'output_path': './output',\n 'pred_save_path': './prediction',\n 'raw_data_path': './kits19',\n 'repeat': 1,\n 'result_path': './preprocess_Result',\n 'resume': False,\n 'resume_ckpt': './',\n 'rst_path': './result_Files/',\n 'run_distribute': False,\n 'run_eval': True,\n 'show_eval': False,\n 'split': 0.8,\n 'train_augment': True,\n 'train_url': '',\n 'transfer_training': False,\n 'weight_decay': 0.0005,\n 'width': 512}\nPlease check the above information for the configurations\n[WARNING] ME(5013:281473310015072,MainProcess):2022-10-17-07:25:18.987.005 [mindspore/train/serialization.py:581] Remove parameter prefix name: net., continue to load.\nforeground:  8101\nbackground:  2712\n============== Starting Evaluating ============\n[WARNING] SESSION(5013,ffff3fff7160,python):2022-10-17-07:25:31.194.055 [mindspore/ccsrc/backend/session/ascend_session.cc:1381] SelectKernel] There are 27 node/nodes used reduce precision to selected the kernel!\nsingle dice coeff is: 0.9847804402983474, IOU is: 0.970017205527196\nsingle dice coeff is: 0.9483567897382124, IOU is: 0.9017856821441713\nsingle dice coeff is: 0.7821650146330401, IOU is: 0.6422586179829256\nsingle dice coeff is: 0.8612625396587829, IOU is: 0.7563310856575403\nsingle dice coeff is: 0.530480510653926, IOU is: 0.36098909507487115\nsingle dice coeff is: 0.47574639948782166, IOU is: 0.31211761568282453\nsingle dice coeff is: 0.9781357315132915, IOU is: 0.9572070985139982\nsingle dice coeff is: 0.9221857792711885, IOU is: 0.855607359353277\nsingle dice coeff is: 0.9281053241741395, IOU is: 0.8658549623441912\nsingle dice coeff is: 0.9710140142113468, IOU is: 0.9436610679076698\nsingle dice coeff is: 0.9835657623503431, IOU is: 0.9676629593122356\nsingle dice coeff is: 0.9108152177340104, IOU is: 0.8362357173583612\nsingle dice coeff is: 0.9401377475088359, IOU is: 0.8870376742818037\nsingle dice coeff is: 0.9908350678340703, IOU is: 0.9818366019789067\nsingle dice coeff is: 0.6957330834582485, IOU is: 0.5334284528990252\nsingle dice coeff is: 0.9777204597574862, IOU is: 0.9564120392407962\nsingle dice coeff is: 0.9082749406129241, IOU is: 0.8319630778859782\nsingle dice coeff is: 0.9580642310827429, IOU is: 0.9195041188367393\nsingle dice coeff is: 0.7335970802957702, IOU is: 0.5792762073441072\nsingle dice coeff is: 0.9301972779506772, IOU is: 0.869503562459426\nsingle dice coeff is: 0.4979810630730319, IOU is: 0.33154113495524123\nsingle dice coeff is: 0.45124128822598714, IOU is: 0.29135673930067296\nsingle dice coeff is: 0.9730690498160922, IOU is: 0.9475506115010268\nsingle dice coeff is: 0.9388108548279308, IOU is: 0.8846781547842774\nsingle dice coeff is: 0.7237603454310984, IOU is: 0.5671037902952294\nsingle dice coeff is: 0.6695772095399677, IOU is: 0.5032815239946709\nsingle dice coeff is: 0.6136719075113504, IOU is: 0.4426599380307766\nsingle dice coeff is: 0.8910539914257102, IOU is: 0.8035143140749376\nsingle dice coeff is: 0.8916308797443172, IOU is: 0.8044530142978291\nsingle dice coeff is: 0.2431810817832133, IOU is: 0.1384212563182368\nsingle dice coeff is: 0.6739527439003957, IOU is: 0.5082418750917974\nsingle dice coeff is: 0.9544240183840931, IOU is: 0.9128212919629799\nsingle dice coeff is: 0.2843740003758519, IOU is: 0.16575524061663285\nsingle dice coeff is: 0.8567714010081401, IOU is: 0.7494313926048316\nsingle dice coeff is: 0.9371080500756219, IOU is: 0.881658808444541\nsingle dice coeff is: 0.726282107615976, IOU is: 0.570206410664916\nsingle dice coeff is: 0.43185899591309007, IOU is: 0.2753955127680313\nsingle dice coeff is: 0.6826715516810926, IOU is: 0.5182242534519584\nsingle dice coeff is: 0.010178399195252555, IOU is: 0.0051152320344377035\nsingle dice coeff is: 0.9429058009996182, IOU is: 0.8919789758483744\nsingle dice coeff is: 0.014447403473492115, IOU is: 0.007276263292529323\nsingle dice coeff is: 0.6974507587692633, IOU is: 0.5354505892692891\nsingle dice coeff is: 0.2838502608239305, IOU is: 0.16539947205318353\nsingle dice coeff is: 0.9631878272617164, IOU is: 0.928989698025901\nsingle dice coeff is: 0.25045472270163316, IOU is: 0.14315418180453338\nsingle dice coeff is: 0.9433679978152545, IOU is: 0.8928065739677573\nsingle dice coeff is: 0.9439051251740952, IOU is: 0.8937692509204687\nsingle dice coeff is: 0.4365876891527822, IOU is: 0.2792530710700327\nsingle dice coeff is: 0.3751868543955262, IOU is: 0.2309107699002193\nsingle dice coeff is: 0.01935950468223111, IOU is: 0.009774365781168743\nsingle dice coeff is: 0.9376218724746573, IOU is: 0.8825688784262841\nsingle dice coeff is: 0.9293322762245294, IOU is: 0.8679931743411923\nsingle dice coeff is: 0.49507454863620415, IOU is: 0.328969483629609\nsingle dice coeff is: 0.9818991966244055, IOU is: 0.9644420212309432\nsingle dice coeff is: 0.880124080979943, IOU is: 0.7859121408290413\nsingle dice coeff is: 0.9673125830542716, IOU is: 0.9366944606676733\nsingle dice coeff is: 0.2825988222114328, IOU is: 0.16455026691860353\nsingle dice coeff is: 0.9077192325511299, IOU is: 0.8310310495269435\nsingle dice coeff is: 0.9560993661476994, IOU is: 0.9158911635290528\nsingle dice coeff is: 0.8666187484970648, IOU is: 0.7646312724406491\nsingle dice coeff is: 0.9563839923081193, IOU is: 0.9164136859334993\nsingle dice coeff is: 0.9231997788984497, IOU is: 0.8573547449256932\nsingle dice coeff is: 0.9781747720224455, IOU is: 0.9572818768220237\nsingle dice coeff is: 0.9910669826524573, IOU is: 0.9822921498376028\nsingle dice coeff is: 0.9264570915789168, IOU is: 0.8629902766918806\nsingle dice coeff is: 0.3034351784180944, IOU is: 0.17885268783020405\nsingle dice coeff is: 0.8995146361423323, IOU is: 0.8173799177020875\nsingle dice coeff is: 0.9703963262330497, IOU is: 0.9424950113889142\nsingle dice coeff is: 0.4893535222614229, IOU is: 0.3239364930661874\nsingle dice coeff is: 0.9132037708643005, IOU is: 0.8402713833397707\nsingle dice coeff is: 0.748418756922123, IOU is: 0.5979785659631799\nsingle dice coeff is: 0.8875475615333064, IOU is: 0.7978296696950242\nsingle dice coeff is: 0.8730443403006066, IOU is: 0.7746927155354846\nsingle dice coeff is: 0.9283770399293558, IOU is: 0.8663280598879244\nsingle dice coeff is: 0.9720081949309406, IOU is: 0.9455408011405714\nsingle dice coeff is: 0.9347475125749197, IOU is: 0.8774891620618355\nsingle dice coeff is: 0.9137620728598342, IOU is: 0.8412172416641501\nsingle dice coeff is: 0.9871396431752809, IOU is: 0.9746058640007675\nsingle dice coeff is: 0.9492167160580544, IOU is: 0.9033420407080794\nsingle dice coeff is: 0.9801615675627756, IOU is: 0.9610949503249958\nsingle dice coeff is: 0.9768547868193262, IOU is: 0.9547567385694515\nsingle dice coeff is: 0.398727341756644, IOU is: 0.2490065259679509\nsingle dice coeff is: 0.871381296535741, IOU is: 0.7720776679148272\nsingle dice coeff is: 0.8941718155865794, IOU is: 0.8085992274296093\nsingle dice coeff is: 0.06190222031243928, IOU is: 0.03193967866905997\nsingle dice coeff is: 0.9899173513832039, IOU is: 0.9800359928356295\nsingle dice coeff is: 0.9427048674820039, IOU is: 0.8916194149469976\nsingle dice coeff is: 0.9505776784782847, IOU is: 0.9058104244437064\nsingle dice coeff is: 0.9664677524992673, IOU is: 0.9351113667099992\nsingle dice coeff is: 0.7035931803508977, IOU is: 0.5427256087262321\nsingle dice coeff is: 0.9709737287536601, IOU is: 0.943584975316162\nsingle dice coeff is: 0.8973780927123791, IOU is: 0.8138583922387971\nsingle dice coeff is: 0.9587512829136728, IOU is: 0.9207706738851956\nsingle dice coeff is: 0.9947894972834428, IOU is: 0.9896330117871313\nsingle dice coeff is: 0.9581476104665829, IOU is: 0.9196577366354936\nsingle dice coeff is: 0.9473920996395219, IOU is: 0.9000427408107767\nsingle dice coeff is: 0.9493738905028116, IOU is: 0.9036267820882212\nsingle dice coeff is: 0.984846418026594, IOU is: 0.9701452425672413\nsingle dice coeff is: 0.9867093280798522, IOU is: 0.9737673062854463\nsingle dice coeff is: 0.7600601436823695, IOU is: 0.6129814601972662\nsingle dice coeff is: 0.9188673327877571, IOU is: 0.8499117274451659\nsingle dice coeff is: 0.8356787777809918, IOU is: 0.7177390241056698\nsingle dice coeff is: 0.626002714585944, IOU is: 0.45560695150667435\nsingle dice coeff is: 0.9230313919999776, IOU is: 0.8570643425847734\nsingle dice coeff is: 0.9781645497652794, IOU is: 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dice coeff is: 0.9116452843074542, IOU is: 0.8376361779508188\nsingle dice coeff is: 0.9716236439222304, IOU is: 0.9448132857001942\nsingle dice coeff is: 0.9351672245038277, IOU is: 0.8782291886799548\nsingle dice coeff is: 0.9023039184953966, IOU is: 0.8219979406855635\nsingle dice coeff is: 0.9345160977047983, IOU is: 0.8770813859240103\nsingle dice coeff is: 0.9810719133152207, IOU is: 0.9628470606863644\nsingle dice coeff is: 0.9164984064327263, IOU is: 0.8458671513488842\nsingle dice coeff is: 0.008160439202196605, IOU is: 0.004096935999668596\nsingle dice coeff is: 0.5275396585647179, IOU is: 0.35827087746926894\nsingle dice coeff is: 0.01053425074779154, IOU is: 0.005295014881131333\nsingle dice coeff is: 0.9686731494251597, IOU is: 0.9392494230953468\nsingle dice coeff is: 0.5695334501207371, IOU is: 0.3981452416128206\nsingle dice coeff is: 0.9030451023596845, IOU is: 0.8232290172569949\nsingle dice coeff is: 0.893459668563298, IOU is: 0.8074352494709833\nsingle dice coeff 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0.798318824592829\nsingle dice coeff is: 0.12162424958524506, IOU is: 0.06474969108730765\nsingle dice coeff is: 0.0016771855236287578, IOU is: 0.0008392965898596507\nsingle dice coeff is: 0.0029858597024078905, IOU is: 0.001495162023220798\nsingle dice coeff is: 0.918105527815342, IOU is: 0.8486091309454806\nsingle dice coeff is: 0.6073037996840237, IOU is: 0.4360633708530533\nsingle dice coeff is: 0.3214223247027151, IOU is: 0.1914849276461332\nsingle dice coeff is: 0.9594150771729105, IOU is: 0.9219959429801708\nsingle dice coeff is: 0.9327412673335486, IOU is: 0.8739598363399447\nsingle dice coeff is: 0.014976425365226809, IOU is: 0.007544709068748636\nsingle dice coeff is: 0.0023988838039272526, IOU is: 0.0012008822905021806\nsingle dice coeff is: 0.964851724697321, IOU is: 0.932090356248912\nsingle dice coeff is: 0.9513495187881438, IOU is: 0.9072131618999801\nsingle dice coeff is: 0.3737968260675719, IOU is: 0.22985862533011137\nsingle dice coeff is: 0.907962287803598, IOU is: 0.8314385828099513\nsingle dice coeff is: 0.9873826995235933, IOU is: 0.9750798243907729\nsingle dice coeff is: 0.5653967511375477, IOU is: 0.39411366981489193\nsingle dice coeff is: 0.9659156424357129, IOU is: 0.934078187499963\nsingle dice coeff is: 0.9857779856895965, IOU is: 0.9719548301856307\nsingle dice coeff is: 0.9919345041140053, IOU is: 0.9839980717147632\nsingle dice coeff is: 0.970134588270812, IOU is: 0.942001330680593\nsingle dice coeff is: 0.9553370194468986, IOU is: 0.9144930348169237\nsingle dice coeff is: 0.9877054398452566, IOU is: 0.9757095204524977\nsingle dice coeff is: 0.8253968373655016, IOU is: 0.7027027200524749\nsingle dice coeff is: 0.9437967601173404, IOU is: 0.8935749526977336\nsingle dice coeff is: 0.34110490279428435, IOU is: 0.20562174387569773\nsingle dice coeff is: 0.9712691843391617, IOU is: 0.9441431806582323\nsingle dice coeff is: 0.0335186915290263, IOU is: 0.01704500896328812\nsingle dice coeff is: 0.9594979951027623, IOU is: 0.9221491074373513\nsingle dice coeff is: 0.5905421135556984, IOU is: 0.4189852845092688\nsingle dice coeff is: 0.7865252882160421, IOU is: 0.6481596036391666\nsingle dice coeff is: 0.8466291990719783, IOU is: 0.734047713355294\nsingle dice coeff is: 0.8465113245464075, IOU is: 0.7338705117443216\nsingle dice coeff is: 0.9210036083783006, IOU is: 0.8535743173284015\nsingle dice coeff is: 0.0013985377013590278, IOU is: 0.0006997581697706429\nsingle dice coeff is: 0.9477301956735951, IOU is: 0.9006532276959811\nsingle dice coeff is: 0.8321456810760353, IOU is: 0.7125423673072134\n============== Cross valid dice coeff is: 0.8040095087199505\n============== Cross valid IOU is: 0.7277493074684571\n\n", "output_type": "stream"}]}, {"cell_type": "code", "source": "!python pred.py --data_path=kits19 --pred_save_path=prediction --config_path=unet_simple_config.yaml --checkpoint_file_path=output/checkpoint/ckpt_0/best.ckpt --device_target=Ascend", "metadata": {"trusted": true}, "execution_count": 13, "outputs": [{"name": "stdout", "text": "{'enable_modelarts': 'Whether training on modelarts, default: False', 'data_url': 'Dataset url for obs', 'train_url': 'Training output url for obs', 'checkpoint_url': 'The location of checkpoint for obs', 'data_path': 'Dataset path for local', 'output_path': 'Training output path for local', 'load_path': 'The location of checkpoint for obs', 'device_target': 'Target device type, available: [Ascend, GPU, CPU]', 'enable_profiling': 'Whether enable profiling while training, default: False', 'num_classes': 'Class for dataset', 'batch_size': 'Batch size for training and evaluation', 'weight_decay': 'Weight decay.', 'keep_checkpoint_max': 'keep the last keep_checkpoint_max checkpoint', 'checkpoint_path': 'The location of the checkpoint file.', 'checkpoint_file_path': 'The location of the checkpoint file.', 'train_augment': 'Whether apply data augment when training.'}\n{'FixedLossScaleManager': 1024.0,\n 'batch_size': 16,\n 'checkpoint_file_path': 'output/checkpoint/ckpt_0/best.ckpt',\n 'checkpoint_path': './checkpoint/',\n 'checkpoint_url': '',\n 'color': [[0, 0, 0],\n           [255, 0, 0],\n           [0, 255, 0],\n           [0, 0, 255],\n           [0, 255, 255],\n           [255, 0, 255],\n           [255, 255, 255]],\n 'config_path': 'unet_simple_config.yaml',\n 'crop': 'None',\n 'cross_valid_ind': 1,\n 'data_path': 'kits19',\n 'data_url': '',\n 'dataset': 'kits19',\n 'device_target': 'Ascend',\n 'distribute_epochs': 2400,\n 'enable_modelarts': False,\n 'enable_profiling': False,\n 'epochs': 10,\n 'eval_activate': 'Softmax',\n 'eval_interval': 1,\n 'eval_metrics': 'dice_coeff',\n 'eval_resize': False,\n 'eval_start_epoch': 0,\n 'file_format': 'MINDIR',\n 'file_name': 'unet',\n 'filter_weight': ['final1.weight'],\n 'height': 512,\n 'image_size': [512, 512],\n 'include_background': False,\n 'keep_checkpoint_max': 10,\n 'load_path': './output/checkpoint_path/',\n 'loss_scale': 1024.0,\n 'lr': 0.0001,\n 'model_name': 'unet_simple',\n 'num_channels': 1,\n 'num_classes': 3,\n 'output_path': './output',\n 'pred_save_path': 'prediction',\n 'raw_data_path': './kits19',\n 'repeat': 1,\n 'result_path': './preprocess_Result',\n 'resume': False,\n 'resume_ckpt': './',\n 'rst_path': './result_Files/',\n 'run_distribute': False,\n 'run_eval': True,\n 'show_eval': False,\n 'split': 0.8,\n 'train_augment': True,\n 'train_url': '',\n 'transfer_training': False,\n 'weight_decay': 0.0005,\n 'width': 512}\nPlease check the above information for the configurations\n[WARNING] ME(6307:281473046130272,MainProcess):2022-10-17-07:28:26.906.044 [mindspore/train/serialization.py:581] Remove parameter prefix name: net., continue to load.\n============== Starting Prediction ============\nprocessing img_path ./kits19/case_00210/imaging.nii.gz img_arr shape(512, 512, 42) \n[WARNING] SESSION(6307,ffff317fa160,python):2022-10-17-07:28:39.236.397 [mindspore/ccsrc/backend/session/ascend_session.cc:1381] SelectKernel] There are 27 node/nodes used reduce precision to selected the kernel!\nprediction/case_00210/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00211/imaging.nii.gz img_arr shape(512, 512, 95) \nprediction/case_00211/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00212/imaging.nii.gz img_arr shape(512, 512, 87) \nprediction/case_00212/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00213/imaging.nii.gz img_arr shape(512, 512, 636) \nprediction/case_00213/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00214/imaging.nii.gz img_arr shape(512, 512, 505) \nprediction/case_00214/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00215/imaging.nii.gz img_arr shape(512, 512, 82) \nprediction/case_00215/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00216/imaging.nii.gz img_arr shape(512, 512, 743) \nprediction/case_00216/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00217/imaging.nii.gz img_arr shape(512, 512, 139) \nprediction/case_00217/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00218/imaging.nii.gz img_arr shape(512, 512, 164) \nprediction/case_00218/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00219/imaging.nii.gz img_arr shape(512, 512, 167) \nprediction/case_00219/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00220/imaging.nii.gz img_arr shape(512, 512, 174) \nprediction/case_00220/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00221/imaging.nii.gz img_arr shape(512, 512, 141) \nprediction/case_00221/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00222/imaging.nii.gz img_arr shape(512, 512, 91) \nprediction/case_00222/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00223/imaging.nii.gz img_arr shape(512, 512, 479) \nprediction/case_00223/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00224/imaging.nii.gz img_arr shape(512, 512, 97) \nprediction/case_00224/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00225/imaging.nii.gz img_arr shape(512, 512, 103) \nprediction/case_00225/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00226/imaging.nii.gz img_arr shape(512, 512, 160) \nprediction/case_00226/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00227/imaging.nii.gz img_arr shape(512, 512, 145) \nprediction/case_00227/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00228/imaging.nii.gz img_arr shape(512, 512, 102) \nprediction/case_00228/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00229/imaging.nii.gz img_arr shape(512, 512, 266) \nprediction/case_00229/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00230/imaging.nii.gz img_arr shape(512, 512, 93) \nprediction/case_00230/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00231/imaging.nii.gz img_arr shape(512, 512, 165) \nprediction/case_00231/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00232/imaging.nii.gz img_arr shape(512, 512, 101) \nprediction/case_00232/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00233/imaging.nii.gz img_arr shape(512, 512, 96) \nprediction/case_00233/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00234/imaging.nii.gz img_arr shape(512, 512, 140) \nprediction/case_00234/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00235/imaging.nii.gz img_arr shape(512, 512, 159) \nprediction/case_00235/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00236/imaging.nii.gz img_arr shape(512, 512, 64) \nprediction/case_00236/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00237/imaging.nii.gz img_arr shape(512, 512, 175) \nprediction/case_00237/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00238/imaging.nii.gz img_arr shape(512, 512, 96) \nprediction/case_00238/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00239/imaging.nii.gz img_arr shape(512, 512, 92) \nprediction/case_00239/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00240/imaging.nii.gz img_arr shape(512, 512, 193) \nprediction/case_00240/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00241/imaging.nii.gz img_arr shape(512, 512, 99) \nprediction/case_00241/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00242/imaging.nii.gz img_arr shape(512, 512, 82) \nprediction/case_00242/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00243/imaging.nii.gz img_arr shape(512, 512, 92) \nprediction/case_00243/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00244/imaging.nii.gz img_arr shape(512, 512, 88) \nprediction/case_00244/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00245/imaging.nii.gz img_arr shape(512, 512, 149) \nprediction/case_00245/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00246/imaging.nii.gz img_arr shape(512, 512, 598) \nprediction/case_00246/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00247/imaging.nii.gz img_arr shape(512, 512, 284) \nprediction/case_00247/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00248/imaging.nii.gz img_arr shape(512, 512, 66) \nprediction/case_00248/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00249/imaging.nii.gz img_arr shape(512, 512, 258) \nprediction/case_00249/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00250/imaging.nii.gz img_arr shape(512, 512, 210) \nprediction/case_00250/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00251/imaging.nii.gz img_arr shape(512, 512, 45) \nprediction/case_00251/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00252/imaging.nii.gz img_arr shape(512, 512, 51) \nprediction/case_00252/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00253/imaging.nii.gz img_arr shape(512, 512, 491) \nprediction/case_00253/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00254/imaging.nii.gz img_arr shape(512, 512, 250) \nprediction/case_00254/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00255/imaging.nii.gz img_arr shape(512, 512, 180) \nprediction/case_00255/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00256/imaging.nii.gz img_arr shape(512, 512, 75) \nprediction/case_00256/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00257/imaging.nii.gz img_arr shape(512, 512, 32) \nprediction/case_00257/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00258/imaging.nii.gz img_arr shape(512, 512, 107) \nprediction/case_00258/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00259/imaging.nii.gz img_arr shape(512, 512, 82) \nprediction/case_00259/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00260/imaging.nii.gz img_arr shape(512, 512, 54) \nprediction/case_00260/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00261/imaging.nii.gz img_arr shape(512, 512, 615) \nprediction/case_00261/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00262/imaging.nii.gz img_arr shape(512, 512, 63) \nprediction/case_00262/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00263/imaging.nii.gz img_arr shape(512, 512, 653) \nprediction/case_00263/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00264/imaging.nii.gz img_arr shape(512, 512, 411) \nprediction/case_00264/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00265/imaging.nii.gz img_arr shape(512, 512, 91) \nprediction/case_00265/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00266/imaging.nii.gz img_arr shape(512, 512, 88) \nprediction/case_00266/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00267/imaging.nii.gz img_arr shape(512, 512, 46) \nprediction/case_00267/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00268/imaging.nii.gz img_arr shape(512, 512, 177) \nprediction/case_00268/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00269/imaging.nii.gz img_arr shape(512, 512, 101) \nprediction/case_00269/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00270/imaging.nii.gz img_arr shape(512, 512, 93) \nprediction/case_00270/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00271/imaging.nii.gz img_arr shape(512, 512, 468) \nprediction/case_00271/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00272/imaging.nii.gz img_arr shape(512, 512, 673) \nprediction/case_00272/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00273/imaging.nii.gz img_arr shape(512, 512, 238) \nprediction/case_00273/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00274/imaging.nii.gz img_arr shape(512, 512, 125) \nprediction/case_00274/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00275/imaging.nii.gz img_arr shape(512, 512, 94) \nprediction/case_00275/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00276/imaging.nii.gz img_arr shape(512, 512, 727) \nprediction/case_00276/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00277/imaging.nii.gz img_arr shape(512, 512, 79) \nprediction/case_00277/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00278/imaging.nii.gz img_arr shape(512, 512, 165) \nprediction/case_00278/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00279/imaging.nii.gz img_arr shape(512, 512, 60) \nprediction/case_00279/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00280/imaging.nii.gz img_arr shape(512, 512, 79) \nprediction/case_00280/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00281/imaging.nii.gz img_arr shape(512, 512, 266) \nprediction/case_00281/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00282/imaging.nii.gz img_arr shape(512, 512, 86) \nprediction/case_00282/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00283/imaging.nii.gz img_arr shape(512, 512, 337) \nprediction/case_00283/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00284/imaging.nii.gz img_arr shape(512, 512, 244) \nprediction/case_00284/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00285/imaging.nii.gz img_arr shape(512, 512, 41) \nprediction/case_00285/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00286/imaging.nii.gz img_arr shape(512, 512, 106) \nprediction/case_00286/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00287/imaging.nii.gz img_arr shape(512, 512, 54) \nprediction/case_00287/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00288/imaging.nii.gz img_arr shape(512, 512, 276) \nprediction/case_00288/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00289/imaging.nii.gz img_arr shape(512, 512, 86) \nprediction/case_00289/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00290/imaging.nii.gz img_arr shape(512, 512, 683) \nprediction/case_00290/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00291/imaging.nii.gz img_arr shape(512, 512, 131) \nprediction/case_00291/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00292/imaging.nii.gz img_arr shape(512, 512, 95) \nprediction/case_00292/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00293/imaging.nii.gz img_arr shape(512, 512, 591) \nprediction/case_00293/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00294/imaging.nii.gz img_arr shape(512, 512, 623) \nprediction/case_00294/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00295/imaging.nii.gz img_arr shape(512, 512, 564) \nprediction/case_00295/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00296/imaging.nii.gz img_arr shape(512, 512, 83) \nprediction/case_00296/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00297/imaging.nii.gz img_arr shape(512, 512, 102) \nprediction/case_00297/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00298/imaging.nii.gz img_arr shape(512, 512, 617) \nprediction/case_00298/segmentation.nii.gz  saved!\nprocessing img_path ./kits19/case_00299/imaging.nii.gz img_arr shape(512, 512, 624) \nprediction/case_00299/segmentation.nii.gz  saved!\n============== Ending Prediction ============\n\n", "output_type": "stream"}]}, {"cell_type": "code", "source": "#\u5bfc\u51fa\u4ee3\u7801\u548c\u6570\u636e\nimport os\nimport moxing as mox\ndata_obs_url = 'obs://bdci2022/unet_result' \ndata_local_url = './'\nmox.file.copy_parallel(data_local_url,data_obs_url)\nprint('\u4ee3\u7801\u5bfc\u51fa\u5b8c\u6210....')", "metadata": {"trusted": true}, "execution_count": 9, "outputs": [{"name": "stderr", "text": "INFO:root:pid: None.\t1000/16158\nINFO:root:pid: None.\t2000/16158\nINFO:root:pid: None.\t3000/16158\nINFO:root:pid: None.\t4000/16158\nINFO:root:pid: None.\t5000/16158\nINFO:root:pid: None.\t6000/16158\nINFO:root:pid: None.\t7000/16158\nINFO:root:pid: None.\t8000/16158\nINFO:root:pid: None.\t9000/16158\nINFO:root:pid: None.\t10000/16158\nINFO:root:pid: None.\t11000/16158\nINFO:root:pid: None.\t12000/16158\nINFO:root:pid: None.\t13000/16158\nINFO:root:pid: None.\t14000/16158\nINFO:root:pid: None.\t15000/16158\nINFO:root:pid: None.\t16000/16158\n", "output_type": "stream"}, {"name": "stdout", "text": "\u4ee3\u7801\u5bfc\u51fa\u5b8c\u6210....\n", "output_type": "stream"}]}, {"cell_type": "code", "source": "", "metadata": {}, "execution_count": null, "outputs": []}]}